Tanada et al.
quenched by addition of H2O and acidified with 10% HCl. The
mixture was extracted with EtOAc. The organic layer was dried
over Na2SO4 and concentrated under reduced pressure. The residue
was dissolved in EtOAc and extracted with 10% NaOH. The
aqueous layer was acidified with concentrated HCl and extracted
with EtOAc. The organic layer was dried over Na2SO4 and
concentrated under reduced pressure. The crude product was
recrystallized from hexane/EtOAc to give 5 (10.3 g, 32%) as an
orange solid: mp 183-184 °C; IR (powder) cm-1 3489, 3377,
1707, 1609, 1572;1H NMR (400 MHz, DMSO-d6) δ 7.12 (d, J )
2.3 Hz, 1H), 7.06 (s, 2H), 6.75 (d, J ) 2.1 Hz, 1H); 13C NMR
(100 MHz, CDCl3) δ 166.2, 145.2, 137.8, 133.1, 129.2, 118.9,
115.3.
3-Amino-5-(4-methylpiperazin-1-yl)-2-nitrobenzoic Acid Meth-
yl Ester (6). Under argon, to a solution of 5 (6.75 g, 31.2 mmol)
in absolute MeOH (200 mL) was added H2SO4 (2 mL), and the
mixture was heated at reflux. After 90 h, the reaction mixture was
neutralized with powdered Na2CO3. The mixture was diluted with
H2O and extracted with EtOAc. The organic layer was dried over
Na2SO4 and concentrated under reduced pressure. Column chro-
matography (silica gel, hexane/EtOAc, 2/1 to 1/1) afforded 3-amino-
5-chloro-2-nitrobenzoic acid methyl ester (5.33 g, 74%) as a red
solid. The aqueous layer was acidified with 10% HCl and extracted
with EtOAc. The organic layer was dried over Na2SO4 and
concentrated under reduced pressure to recover 5 (1.19 g, 16%) as
a brown solid: mp 106-107 °C; IR (powder) cm-1 3464, 3352,
1717, 1570, 1290; 1H NMR (500 MHz, DMSO-d6) δ 6.90 (d, J )
2.3 Hz, 1H), 6.80 (d, J ) 2.3 Hz, 1H), 5.86 (br, 2H), 3.90 (s, 3H);
13C NMR (100 MHz, CDCl3) δ 166.3, 144.4, 140.3, 132.8, 129.6,
119.4, 118.1, 53.3; HRMS (ESI) m/z calcd for C8H7ClN2O4Na ([M
+ Na]+) 252.9987, found 252.9983.
Under argon, to a solution of 3-amino-5-chloro-2-nitrobenzoic
acid methyl ester (100 mg, 0.43 mmol) in DMF (2 mL) was added
N-methylpiperazine (273 µL, 2.46 mmol) and potassium carbonate
(341 mg, 2.47 mmol), and the solution was heated at 105 °C. After
3.5 h, the reaction mixture was filtered and concentrated under
reduced pressure. Column chromatography (silica gel, CHCl3/
MeOH, 8/1 to 6/1) afforded 6 (66 mg, 52%) as a red solid: mp
160-161 °C; IR (powder) cm-1 3406, 3263, 1728, 1605, 1572;
1H NMR (270 MHz, CDCl3) δ 6.33 (d, J ) 2.6 Hz, 1H), 6.13 (br,
2H), 5.97 (d, J ) 2.6 Hz, 1H), 3.89 (s, 3H), 3.38 (t, J ) 5.1 Hz,
4H), 2.52 (t, J ) 5.1 Hz, 4H), 2.35 (s, 3H); 13C NMR (100 MHz,
CDCl3) δ 168.6, 153.8, 147.0, 124.3, 110.0, 106.5, 99.2, 54.4, 53.0,
46.7, 46.0; HRMS (ESI) m/z calcd for C13H19N4O4 ([M + H]+)
295.1401, found 295.1448.
2′-(4-Hydroxy-phenyl)-6-(4-methyl-piperazin-1-yl)-1H,3′H-
[2,5′]bibenzoimidazolyl-4-carboxylic Acid (7). A solution of 6
(500 mg, 1.07 mmol) in EtOH (25 mL) was hydrogenated over
5% Pd/C (500 mg) at room temperature. After 6.5 h, the reaction
mixture was filtered through a bed of Celite to remove the catalyst
and concentrated under reduced pressure to afford the corresponding
diamine. To a solution of the above product in EtOH (25 mL) was
added a solution of sodium pyrosulfite (168 mg, 0.88 mmol) in
H2O (0.9 mL) and 4 (607 mg, 2.55 mmol), and then the reaction
mixture was heated at reflux. After 20 h, the reaction mixture was
concentrated under reduced pressure. Column chromatography
(silica gel, diethyl ether/MeOH, 3/1 to 3/2) afforded the methyl
ester of 7 (768 mg, 94%) as a yellow solid: mp 269-270 °C; IR
(powder) cm-1 3500-2800, 1612, 1445; 1H NMR (400 MHz,
MeOH-d4) δ 8.28 (s, 1H), 7.98 (d, J ) 8.4 Hz, 1H), 7.96 (d, J )
8.8 Hz, 2H), 7.67 (d, J ) 8.4 Hz, 1H), 7.62 (d, J ) 2.3 Hz, 1H),
7.46 (d, J ) 2.1 Hz, 1H), 6.93 (d, J ) 8.8 Hz, 2H), 4.04 (s, 3H),
3.24 (t, J ) 5.0 Hz, 4H), 2.67 (t, J ) 4.9 Hz, 4H), 2.37 (s, 3H);
13C NMR (125 MHz, DMSO-d6) δ 165.8, 159.6, 154.5, 153.4,
145.3, 128.4, 123.3, 121.8, 120.5, 115.8, 114.7, 52.6, 52.2, 47.3,
42.2; HRMS (ESI) m/z calcd for C27H27N6O3 ([M + H]+) 483.2139,
found 483.2103.
ing on the length of the linker. As an interesting application of
the new ligand, binding to the junction DNA has been achieved.
As a first approach for recognition of highly ordered DNA
structure, this study has represented a reliable molecular basis
to design junction-specific DNA-binding molecules.
Experimental Section
N-Methoxy-N-methyl-3,4-diaminobenzamide (3). Under argon,
a mixture of thionyl chloride (25 mL) and 3,4-dinitrobenzoic acid
(2) (10 g, 47.1 mmol) was heated at 80 °C. After 3 h, the reaction
mixture was concentrated under reduced pressure. The residue was
subjected to toluene azeotrope to give the corresponding acid
chloride as a brown oil. Under argon, to a solution of the above
acid chloride in CH2Cl2 (50 mL) was added pyridine (6.9 mL, 85.3
mmol) and N,O-dimethylhydroxylamine hydrochloride (5.72 g, 58.6
mmol) at 0 °C, and then the mixture was stirred at room
temperature. After 3.5 h, the reaction mixture was diluted with CH2-
Cl2 and washed with H2O and brine. The organic layer was dried
over Na2SO4 and concentrated under reduced pressure. The residue
was recrystallized from diethyl ether to give N-methoxy-N-methyl-
3,4-dinitrobenzamide (7.79 g, 65%) as a pale yellow solid: mp
1
95-96 °C; IR (powder) cm-1 1639, 1535, 1360; H NMR (270
MHz, CDCl3) δ 8.30 (d, J ) 1.6 Hz, 1H), 8.11 (dd, J ) 1.6, 8.3,
1H), 7.96 (d, J ) 8.3 Hz, 1H), 3.59 (s, 3H), 3.43 (s, 3H); 13C NMR
(100 MHz, CDCl3) δ 164.7, 143.4, 142.2, 139.0, 133.5, 125.4,
124.8, 61.7, 33.0.
A solution of the above product (6.37 g, 25 mmol) in EtOH
(200 mL) was hydrogenated over 5% Pd/C (4 g) for 4 h at room
temperature. The reaction mixture was used for the next reaction
without purification.
2-(4-Hydroxyphenyl)-3H-benzoimidazole-5-carbaldehyde (4).
A mixture of the above mixture, a solution of sodium pyrosulfite
(4.54 g, 23.9 mmol) in H2O (6 mL), and p-hydroxybenzaldehyde
(3.36 g, 27.5 mmol) was heated at reflux. After 6 h, the reaction
mixture was cooled to room temperature and filtered through a bed
of Celite to remove the catalyst. The filtrate was concentrated under
reduced pressure. The residue was washed with MeOH to give 2-(4-
hydroxyphenyl)-3H-benzoimidazole-5-carboxylic acid N-methoxy-
N-methylamide (3.69 g, 50%) as a beige powder: mp 281-282
°C; IR (powder) cm-1 3245, 1613, 1576, 1380; 1H NMR (400 MHz,
MeOH-d4) δ 10.00 (s, 0.5H), 9.99 (s, 0.5H), 8.00 (d, J ) 8.6 Hz,
2H), 7.86 (s, 0.5H), 7.75 (s, 0.5H), 7.62-7.42 (m, 3H), 6.91 (d, J
) 8.9 Hz, 2H), 3.61 (s, 3H), 3.39 (s, 3H); 13C NMR (100 MHz,
CDCl3) δ 169.8, 159.5, 153.7, 128.4, 127.4, 122.4, 120.7, 118.4,
117.6, 115.8, 110.5, 60.5, 33.7; HRMS (APCI) m/z calcd for
C16H16N3O3 ([M + H]+) 298.1186, found 298.1179.
Under argon, to a suspension of the above product (972 mg,
3.27 mmol) in THF/diethyl ether (3/1, 120 mL) was added LiAlH4
(380 mg, 13.3 mmol) at -40 °C, and then the reaction mixture
was stirred at 4 °C. After 46 h, the mixture was poured into saturated
NH4Cl/ice (1/1) and stirred for 10 min. The solution was extracted
with EtOAc, and the organic layer was dried over Na2SO4 and
concentrated under reduced pressure. The residue was triturated
with EtOAc/diethyl ether (1/1) to afford 4 (654 mg, 84%) as a pale
yellow powder: mp >300 °C; IR (powder) cm-1 3300-3100, 1611,
1286; 1H NMR (500 MHz, DMSO-d6) δ 10.02 (s, 1H), 8.07-8.06
(m, 1H), 8.03 (d, J ) 8.9 Hz, 2H), 7.73-7.68 (m, 3H), 6.93 (d, J
) 8.7 Hz, 2H); 13C NMR (100 MHz, DMSO-d6) δ 192.5, 159.9,
159.2, 156.2, 152.0, 131.3, 130.9, 128.7, 128.2, 123.4, 123.0, 121.2,
120.4, 115.9, 115.7, 114.9; HRMS (APCI) m/z calcd for C14H11N2O2
([M + H]+) 239.0815, found 239.0809.
3-Amino-5-chloro-2-nitrobenzoic Acid (5). Under argon, to a
solution of potassium tert-butoxide (94 g, 838 mmol) and copper-
(II) acetate monohydrate (2.2 g, 12.1 mmol) in DMF (400 mL)
was added a solution of O-methylhydroxylamine hydrochloride (20
g, 239 mmol) and 3-chloro-6-nitrobenzoic acid (25 g, 124 mmol)
in DMF (400 mL) at 0 °C. After 3 h, the reaction mixture was
A solution of the above methyl ester of 7 (1 g, 2.07 mmol) in 1
M NaOH (33 mL) was heated at 70 °C. After 30 min, the reaction
132 J. Org. Chem., Vol. 71, No. 1, 2006